Restoring Microbiome

gut microbiome, antibiotics, infections, bacteria, probiotics, prebiotics, supplements

Restoring Your Microbiome After Antibiotics

A round of antibiotics can be helpful in fighting a bacterial infection, however, they can also wreak havoc on your system, particularly your microbiome.

Not only do antibiotics eliminate bad bacteria, but also the good – leaving the body susceptible to secondary illnesses and disease (such as thrush and c difficile).

So should you never take antibiotics?

Not necessarily.

Sometimes, they are needed to support the immune system in battling a stubborn or life-threatening infection (they aren’t helpful for viruses) in which knowing how to nurture your microbiome during and after the full course can make all the difference in restoring your health.

Following are recommendations by Dr. Graves for those taking antibiotics:

Saccharomyces Boulardii (also known as Saccahro B)

This probiotic is a helpful yeast that works to crowd out harmful bacteria that may cause c diff and candida overgrowth.  In addition, it can treat diarrhea brought on by the infection or antibiotics.

Klaire Labs™ offers a 3 billion CFU supplement that is carried in the CNMA office.  Take one capsule twice per day throughout the course of antibiotic use.


It’s essential that good bacteria be put back in the body after clearing it and probiotics can help do that – both through food and supplement.

A probiotic of 100 billion CFU (such as ProbioMax® DF) daily during the course of treatment as well as afterwards for 30 days is recommended by Dr. Graves.  Or, 25 billion per day plus a prebiotic supplement can support the microbiome during this time.

After 30 days of 100 billion CFU, Dr. Graves recommends 20-30 billion CFU as maintenance.

When it comes to diet, incorporate fermented foods such as:

  • yogurt
  • kombucha
  • kefir
  • sauerkraut
  • kimchi
  • miso

to continue to nourish the microbiome.


These plant fibers are what good bacteria in your microbiome love to eat.  They can help you restore your own personal microbiome (everyone’s is different) in a way that a general probiotic may not be able to (think of it as fertilizer for your own beneficial bacteria).

As a supplement, these come in a variety of forms such as pill, powder, and wafers.

And as foods, there are a wide variety to choose from such as:

  • onions
  • garlic
  • Jerusalem artichoke
  • leeks
  • bananas
  • berries
  • asparagus
  • tomatoes
  • apples
  • oats
  • barley
  • dandelion greens
  • beans and lentils
  • flaxseed 

Although data is shifting on when to take prebiotics and probiotics (such as if they should be taken during the course of antibiotic treatment and after or just after), it may be best to start this regimen as soon as possible when taking antibiotics.

Liver Supplement

The liver detoxes medications which makes support for processing antibiotics important.  Taking a liver supplement such as SeekingHealth® Liver Nutrients may be helpful for proper liver function.

If you live in Castle Rock, Castle Pines, Lone Tree, Highlands Ranch, Centennial, Parker, Larkspur, Monument, Colorado Springs, or the greater Denver metro area and are in need of naturopathic care during and/or after a course of antibiotics, the CNMA office can help both kids and adults restore their health.

For additional information or to purchase supplements, please call us at (303) 688-6698 or click here to schedule a free 15 minute phone consultation with Dr. Graves to discuss further.

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